NAME

Bio::FastParsers::Blast::Xml - Front-end class for XML BLAST parser

VERSION

version 0.221230

SYNOPSIS

use aliased 'Bio::FastParsers::Blast::Xml';

# open and parse BLAST report in XML format
my $infile = 'test/blastp.xml';
my $report = Xml->new( file => $infile );

# get main container
my $bo = $report->blast_output;

# examine report content
say $bo->program;               # blastp
say $bo->version;               # BLASTP 2.2.25+
say $bo->db;                    # mcl-db-22species

# get evalue threshold...
say $bo->parameters->expect;    # 10

# ...or equivalently
my $param = $bo->parameters;
say $param->expect;             # 10
say $param->matrix;             # BLOSUM62

# get the number of iterations (= queries)
say $bo->count_iterations;      # 3

# loop through iterations (or queries), hits and hsps
# this is extremely fast because no data is moved around
for my $iter ($bo->all_iterations) {
    say $iter->count_hits;      # always available!
    for my $hit ($iter->all_hits) {
        for my $hsp ($hit->all_hsps) {
            # ...
        }
    }
}

# ...or nearly equivalently (still ultra-fast)
# here the container is altered by each iterator call
while (my $iter = $bo->next_iteration) {
    say $iter->count_hits;      # here too!
    while (my $hit = $iter->next_hit) {
        while (my $hsp = $hit->next_hsp) {
            # ...
        }
    }
    say $iter->count_hits;      # 0 (exhausted)
}

DESCRIPTION

This module implements a parser for the XML output format of the BLAST program (e.g., -outfmt 5). It provides methods for iterating over and querying all elements of the XML tree. The hierarchy is as follows:

Bio::FastParsers::Blast::Xml

Bio::FastParsers::Blast::Xml::BlastOutput

Bio::FastParsers::Blast::Xml::Statistics

Bio::FastParsers::Blast::Xml::Parameters

Bio::FastParsers::Blast::Xml::Iteration's

Bio::FastParsers::Blast::Xml::Hit's

Bio::FastParsers::Blast::Xml::Hsp's

Documentation is autogenerated.

ATTRIBUTES

file

Path to BLAST report file in XML format to be parsed

blast_output

Bio::FastParsers::Blast::Xml::BlastOutput composed object

AUTHOR

Denis BAURAIN <denis.baurain@uliege.be>

CONTRIBUTOR

Aymeric NAOME <aymeric.naome@gmail.com>

COPYRIGHT AND LICENSE

This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.